shameless self-plug: we break out of R to do this, and after many painful years developing and maintaining idiosyncratic Makefiles, we are now using Taverna to (visually) glue together UNIX commands (including R scripts) -- the benefits of which (over make and brethren) is that you can actually *see* the dependencies and overall workflow (nesting workflows also makes it easier to manage complexity).
see TavernaPBS: http://cphg.virginia.edu/mackey/projects/sequencing-pipelines/tavernapbs/ while designed to automate job submission to a PBS queuing system, you can also use it to simply execute non-PBS jobs. -- Aaron J. Mackey, PhD Assistant Professor Center for Public Health Genomics University of Virginia amac...@virginia.edu http://www.cphg.virginia.edu/mackey On Thu, Apr 19, 2012 at 3:27 PM, Sean Davis <sdav...@mail.nih.gov> wrote: > There are numerous tools like scons, make, ruffus, ant, rake, etc. > that can be used to build complex pipelines based on task > dependencies. These tools are written in a variety of languages, but > I have not seen such a thing for R. Is anyone aware of a package > available? The goal is to be able to develop robust bioinformatic > pipelines driven by scripts written in R. > > Thanks, > Sean > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
